Iratxe Montes

SNP Discovery in European Anchovy (Engraulis encrasicolus, L) by High-Throughput Transcriptome and Genome Sequencing

Increased throughput in sequencing technologies has facilitated the acquisition of detailed genomic information in non-model species. The focus of this research was to discover and validate SNPs derived from the European anchovy (Engraulis encrasicolus) transcriptome, a species with no available reference genome, using next generation sequencing technologies. A cDNA library was constructed from four tissues of ten fish individuals corresponding to three populations of E. encrasicolus, and Roche 454 GS FLX Titanium sequencing yielded 19,367 contigs. Additionally, the European anchovy genome was sequenced for the same ten individuals using an Illumina HiSeq2000. Using a computational pipeline for combining transcriptome and genome information, a total of 18,994 SNPs met the necessary minor allele frequency and depth filters. A series of further stringent filters were applied to identify those SNPs likely to succeed in genotyping assays, and for filtering of those in potential duplicated genome regions. A novel method for detecting potential intron-exon boundaries in areas of putative SNPs has also been applied in silico to improve genotyping success. In all, 2,317 filtered putative transcriptome SNPs suitable for genotyping primer design were identified. From those, a subset of 530 were selected, with the genotyping results showing the highest reported conversion and validation rates (91.3% and 83.2%, respectively) reported to date for a non-model species. This study represents a promising strategy to discover genotypable SNPs in the exome of non-model organisms. The genomic resource generated for E. encrasicolus, both in terms of sequences and novel markers, will be informative for research into this species with applications including traceability studies, population genetic analyses and aquaculture.

New Nuclear SNP Markers Unravel the Genetic Structure and Effective Population Size of Albacore Tuna (Thunnus alalunga)

In the present study we have investigated the population genetic structure of albacore (Thunnus alalunga, Bonnaterre 1788) and assessed the loss of genetic diversity, likely due to overfishing, of albacore population in the North Atlantic Ocean. For this purpose, 1,331 individuals from 26 worldwide locations were analyzed by genotyping 75 novel nuclear SNPs. Our results indicated the existence of four genetically homogeneous populations delimited within the Mediterranean Sea, the Atlantic Ocean, the Indian Ocean and the Pacific Ocean. Current definition of stocks allows the sustainable management of albacore since no stock includes more than one genetic entity. In addition, short- and long-term effective population sizes were estimated for the North Atlantic Ocean albacore population, and results showed no historical decline for this population. Therefore, the genetic diversity and, consequently, the adaptive potential of this population have not been significantly affected by overfishing.

Insights on the drivers of genetic divergence in the European anchovy

Anchovies represent the largest world’s marine fish catches and the current threats on their populations impose a sustainable exploitment based on sound scientific information. In the European anchovy (Engraulis encrasicolus), the existence of several populations has been proposed but a global view is missing. Using a multidisciplinary approach, here we assessed the divergence among different ecotypes and its possible causes. SNPs have revealed two functionally distinct ecotypes overlapping in the Central Mediterranean, with one ecotype confined near the river estuaries. The same SNPs outliers also segregated two distinct populations in the near Atlantic, despite their large spatial distance. In addition, while most studies suggested that adaptation to low salinity is key to divergence, here we show that the offshore ecotype has higher environmental tolerance and an opportunistic feeding behaviour, as assessed by the study of environmental conditions, anchovy diet and trophic levels, and passive egg dispersal. These results provide insights into the anchovy evolutionary history, stressing the importance of behaviour in shaping ecotypes.

Hygroregulation, a key ability for eusocial insects: Native Western European bees as a case study

Sociality has brought many advantages to various hymenoptera species, including their ability of regulating physical factors in their nest (e.g., temperature). Although less studied, humidity is known to be important for egg, larval and pupal development. Two subspecies of Apis mellifera of the M branch, also called black bees, were used as models to test the “hygroregulation hypothesis”, by means of monitoring hygrometry in hives during one year in four conservation centers: two in France (A. m. mellifera) and two in Portugal (A. m. iberiensis). We investigated the ability of both subspecies to regulate the hygrometry daily, but also during the seasons and one complete year. Our data and statistical analysis probed the capacity of the bees to regulate humidity in their hive, regardless of the day, season or subspecies. Furthermore, the study showed that humidity in beehives is very stable even during winter, when brood is absent, and when temperature is known to be less stable in the beehives. These results would support that hygrometry could prevail over temperature in maintaining nest homeostasis, maybe because of a bigger importance of hygrometry for all the population during a year, or because of the ‘imprint’ of the evolutionary history of this hymenopteran lineage.

Development of gene-associated single nucleotide polymorphisms for Japanese anchovy Engraulis japonicus through cross-species amplification

Cross-species amplification is a fast and cost-effective approach for the discovery of genetic markers in non-model species that have a phylogenetically close species with developed markers. The present study employed this method to discover new single nucleotide polymorphism (SNP) markers in the Japanese anchovy Engraulis japonicus. We selected 482 mitochondrial and nuclear SNPs described in the European anchovy Engraulis encrasicolus; primer and probe sets developed for this species were used for genotyping 35 individuals of E. japonicus. A total of 451 SNPs (93.6%) were successfully cross-amplified, of which 176 SNPs (36.5%) were polymorphic in E. japonicus. The mean expected heterozygosity was 0.102, and no marker deviated significantly from Hardy–Weinberg proportions. Two mitochondrial SNPs were identified as a set of species diagnosing markers since, compared to four other species from the genus Engraulis, they formed a haplotype only present in E. japonicus. The new SNP set presented here constitutes the first SNP-type marker developed for E. japonicus, which is suitable for a range of applications including traceability and population genetics studies.